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  <div class="section" id="iprpy-high-throughput-computational-framework">
<h1>iprPy High-Throughput Computational Framework<a class="headerlink" href="#iprpy-high-throughput-computational-framework" title="Permalink to this headline">¶</a></h1>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
<p>The iprPy framework is a collection of tools and resources supporting the
design of scientific calculations that</p>
<ul class="simple">
<li><p>are open source with minimum barriers for usage,</p></li>
<li><p>have transparent methodologies supporting knowledge transfer and education,</p></li>
<li><p>produce results that are both human and machine readable,</p></li>
<li><p>allow investigations into method and parameter sensitivity,</p></li>
<li><p>and can be integrated into workflows.</p></li>
</ul>
<p>The framework was originally created to support the NIST Interatomic Potential
Repository by evaluating basic materials properties across multiple classical
interatomic potentials.  Because of this, many of the included calculations
and tools are designed towards molecular dynamics simulations.</p>
</div>
<div class="section" id="documentation-sections">
<h2>Documentation Sections<a class="headerlink" href="#documentation-sections" title="Permalink to this headline">¶</a></h2>
<p><a class="reference internal" href="intro.html"><span class="doc">Introduction to iprPy</span></a></p>
<p>A quick introduction describing why you would want to use the iprPy framework.</p>
<p><a class="reference internal" href="setup.html"><span class="doc">Setup</span></a></p>
<p>Describes the basics of iprPy for performing calculations.</p>
<p><a class="reference internal" href="run/index.html"><span class="doc">Calculations</span></a></p>
<p>Learn about the different components of the iprPy framework and how to run
calculations.</p>
<p><a class="reference internal" href="calculation_styles.html"><span class="doc">Calculation Styles</span></a></p>
<p>Describes the implemented calculations and what input parameters the
calculation scripts use.</p>
<p><a class="reference internal" href="notebook_styles.html"><span class="doc">Jupyter Demonstration Notebooks</span></a></p>
<p>Provides demonstration Jupyter Notebooks for the implemented calculations.</p>
<p><a class="reference internal" href="record_styles.html"><span class="doc">Record Styles</span></a></p>
<p>Describes the implemented record formats for storing calculation data.</p>
<p><a class="reference internal" href="database_styles.html"><span class="doc">Database Styles</span></a></p>
<p>Describes the implemented database types that can be interacted with.</p>
<p><a class="reference internal" href="extend/index.html"><span class="doc">Extending iprPy</span></a></p>
<p>This describes the components of iprPy in more detail for those who want to
contribute to the package by adding content.</p>
<p><a class="reference internal" href="iprPy/index.html"><span class="doc">iprPy package</span></a></p>
<p>The Python docstring information for the functions and classes of iprPy.</p>
</div>
<div class="section" id="package-tutorials">
<h2>Package Tutorials<a class="headerlink" href="#package-tutorials" title="Permalink to this headline">¶</a></h2>
<div class="toctree-wrapper compound">
<p class="caption"><span class="caption-text">Contents:</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="intro.html">Introduction to iprPy</a><ul>
<li class="toctree-l2"><a class="reference internal" href="intro.html#scientific-research-work-process">Scientific research work process</a></li>
<li class="toctree-l2"><a class="reference internal" href="intro.html#complications">Complications</a></li>
<li class="toctree-l2"><a class="reference internal" href="intro.html#its-all-in-the-design">It’s all in the design</a></li>
<li class="toctree-l2"><a class="reference internal" href="intro.html#how-much-extra-work">How much extra work?</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="setup.html">Setup</a><ul>
<li class="toctree-l2"><a class="reference internal" href="setup.html#installing-iprpy">Installing iprPy</a></li>
<li class="toctree-l2"><a class="reference internal" href="setup.html#updating-iprpy">Updating iprPy</a></li>
<li class="toctree-l2"><a class="reference internal" href="setup.html#uninstalling-iprpy">Uninstalling iprPy</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="overview.html">iprPy Package Components</a><ul>
<li class="toctree-l2"><a class="reference internal" href="overview.html#calculations">Calculations</a></li>
<li class="toctree-l2"><a class="reference internal" href="overview.html#records">Records</a></li>
<li class="toctree-l2"><a class="reference internal" href="overview.html#databases">Databases</a></li>
<li class="toctree-l2"><a class="reference internal" href="overview.html#reference-library">Reference library</a></li>
<li class="toctree-l2"><a class="reference internal" href="overview.html#subsets">Subsets</a></li>
<li class="toctree-l2"><a class="reference internal" href="overview.html#buildcombos">buildcombos</a></li>
<li class="toctree-l2"><a class="reference internal" href="overview.html#workflow-scripts">Workflow scripts</a></li>
<li class="toctree-l2"><a class="reference internal" href="overview.html#other-supporting-code">Other supporting code</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="run/index.html">Calculations</a><ul>
<li class="toctree-l2"><a class="reference internal" href="run/single.html">Running a single calculation</a><ul>
<li class="toctree-l3"><a class="reference internal" href="run/single.html#calculation-script">Calculation script</a><ul>
<li class="toctree-l4"><a class="reference internal" href="run/single.html#calculation-input-file-rules">Calculation input file rules</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="run/single.html#call-from-python">Call from Python</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="run/notebook.html">Run a Jupyter Calculation Notebook</a></li>
<li class="toctree-l2"><a class="reference internal" href="run/htp.html">High-Throughput Calculation Execution</a><ul>
<li class="toctree-l3"><a class="reference internal" href="run/htp.html#define-databases-and-run-directories">Define databases and run directories</a></li>
<li class="toctree-l3"><a class="reference internal" href="run/htp.html#copy-references-to-a-database">Copy references to a database</a></li>
<li class="toctree-l3"><a class="reference internal" href="run/htp.html#prepare-calculations">Prepare calculations</a><ul>
<li class="toctree-l4"><a class="reference internal" href="run/htp.html#prepare-input-file-rules">Prepare input file rules</a></li>
<li class="toctree-l4"><a class="reference internal" href="run/htp.html#passing-inputs-as-keyword-arguments">Passing inputs as keyword arguments</a></li>
<li class="toctree-l4"><a class="reference internal" href="run/htp.html#recognized-input-keys">Recognized input keys</a></li>
<li class="toctree-l4"><a class="reference internal" href="run/htp.html#using-buildcombos-functions">Using buildcombos functions</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="run/htp.html#executing-calculations-with-runners">Executing calculations with runners</a><ul>
<li class="toctree-l4"><a class="reference internal" href="run/htp.html#runner-process">Runner process</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="run/htp.html#additional-tools-for-database-access-and-manipulation">Additional tools for database access and manipulation</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="run/inline.html">Command Line Actions</a><ul>
<li class="toctree-l3"><a class="reference internal" href="run/inline.html#define">Define</a></li>
<li class="toctree-l3"><a class="reference internal" href="run/inline.html#build">Build</a></li>
<li class="toctree-l3"><a class="reference internal" href="run/inline.html#prepare">Prepare</a></li>
<li class="toctree-l3"><a class="reference internal" href="run/inline.html#runner">Runner</a></li>
<li class="toctree-l3"><a class="reference internal" href="run/inline.html#other">Other</a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="extend/index.html">Extending iprPy</a><ul>
<li class="toctree-l2"><a class="reference internal" href="extend/addreference.html">Reference Library</a></li>
<li class="toctree-l2"><a class="reference internal" href="extend/addcalculation.html">Adding new calculation styles</a><ul>
<li class="toctree-l3"><a class="reference internal" href="extend/addcalculation.html#files-in-the-calculation-style-directories">Files in the calculation style directories</a><ul>
<li class="toctree-l4"><a class="reference internal" href="extend/addcalculation.html#calc-style-py">calc_[style].py</a></li>
<li class="toctree-l4"><a class="reference internal" href="extend/addcalculation.html#calc-style-in">calc_[style].in</a></li>
<li class="toctree-l4"><a class="reference internal" href="extend/addcalculation.html#style-py">[Style].py</a></li>
<li class="toctree-l4"><a class="reference internal" href="extend/addcalculation.html#init-py">__init__.py</a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="extend/addrecord.html">Adding new record styles</a><ul>
<li class="toctree-l3"><a class="reference internal" href="extend/addrecord.html#files-in-the-record-style-directories">Files in the record style directories</a><ul>
<li class="toctree-l4"><a class="reference internal" href="extend/addrecord.html#style-py">[Style].py</a></li>
<li class="toctree-l4"><a class="reference internal" href="extend/addrecord.html#init-py">__init__.py</a></li>
<li class="toctree-l4"><a class="reference internal" href="extend/addrecord.html#record-style-xsd">record-[style].xsd</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="extend/addrecord.html#record-format">Record format</a><ul>
<li class="toctree-l4"><a class="reference internal" href="extend/addrecord.html#record-format-limitations">Record format limitations</a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="extend/addsubset.html">Adding new subset styles</a><ul>
<li class="toctree-l3"><a class="reference internal" href="extend/addsubset.html#files-in-the-subset-style-directories">Files in the subset style directories</a><ul>
<li class="toctree-l4"><a class="reference internal" href="extend/addsubset.html#style-py">[Style].py</a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="extend/addbuildcombos.html">Adding new buildcombos styles</a></li>
<li class="toctree-l2"><a class="reference internal" href="extend/adddatabase.html">Adding new database styles</a><ul>
<li class="toctree-l3"><a class="reference internal" href="extend/adddatabase.html#files-in-the-calculation-style-directories">Files in the calculation style directories</a><ul>
<li class="toctree-l4"><a class="reference internal" href="extend/adddatabase.html#style-py">[Style].py</a></li>
<li class="toctree-l4"><a class="reference internal" href="extend/adddatabase.html#init-py">__init__.py</a></li>
</ul>
</li>
</ul>
</li>
</ul>
</li>
</ul>
</div>
</div>
<div class="section" id="implemented-content">
<h2>Implemented Content<a class="headerlink" href="#implemented-content" title="Permalink to this headline">¶</a></h2>
<div class="toctree-wrapper compound">
<p class="caption"><span class="caption-text">Contents:</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="calculation_styles.html">Calculation Styles</a><ul>
<li class="toctree-l2"><a class="reference internal" href="calculation/E_vs_r_scan/index.html">E_vs_r_scan</a></li>
<li class="toctree-l2"><a class="reference internal" href="calculation/crystal_space_group/index.html">crystal_space_group</a></li>
<li class="toctree-l2"><a class="reference internal" href="calculation/diatom_scan/index.html">diatom_scan</a></li>
<li class="toctree-l2"><a class="reference internal" href="calculation/dislocation_SDVPN/index.html">dislocation_SDVPN</a></li>
<li class="toctree-l2"><a class="reference internal" href="calculation/dislocation_monopole/index.html">dislocation_monopole</a></li>
<li class="toctree-l2"><a class="reference internal" href="calculation/dislocation_periodic_array/index.html">dislocation_periodic_array</a></li>
<li class="toctree-l2"><a class="reference internal" href="calculation/elastic_constants_static/index.html">elastic_constants_static</a></li>
<li class="toctree-l2"><a class="reference internal" href="calculation/isolated_atom/index.html">isolated_atom</a></li>
<li class="toctree-l2"><a class="reference internal" href="calculation/relax_box/index.html">relax_box</a></li>
<li class="toctree-l2"><a class="reference internal" href="calculation/relax_dynamic/index.html">relax_dynamic</a></li>
<li class="toctree-l2"><a class="reference internal" href="calculation/relax_static/index.html">relax_static</a></li>
<li class="toctree-l2"><a class="reference internal" href="calculation/stacking_fault_map_2D/index.html">stacking_fault_map_2D</a></li>
<li class="toctree-l2"><a class="reference internal" href="calculation/stacking_fault_static/index.html">stacking_fault_static</a></li>
<li class="toctree-l2"><a class="reference internal" href="calculation/surface_energy_static/index.html">surface_energy_static</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="notebook_styles.html">Jupyter Demonstration Notebooks</a><ul>
<li class="toctree-l2"><a class="reference internal" href="notebook/E_vs_r_scan.html">E_vs_r_scan calculation style</a></li>
<li class="toctree-l2"><a class="reference internal" href="notebook/crystal_space_group.html">crystal_space_group calculation style</a></li>
<li class="toctree-l2"><a class="reference internal" href="notebook/diatom_scan.html">diatom_scan calculation style</a></li>
<li class="toctree-l2"><a class="reference internal" href="notebook/dislocation_SDVPN.html">dislocation_SDVPN calculation style</a></li>
<li class="toctree-l2"><a class="reference internal" href="notebook/dislocation_monopole.html">dislocation_monopole calculation style</a></li>
<li class="toctree-l2"><a class="reference internal" href="notebook/dislocation_periodic_array.html">dislocation_periodic_array calculation style</a></li>
<li class="toctree-l2"><a class="reference internal" href="notebook/elastic_constants_static.html">elastic_constants_static calculation style</a></li>
<li class="toctree-l2"><a class="reference internal" href="notebook/isolated_atom.html">isolated_atom calculation style</a></li>
<li class="toctree-l2"><a class="reference internal" href="notebook/phonon.html">phonon calculation style</a></li>
<li class="toctree-l2"><a class="reference internal" href="notebook/point_defect_diffusion.html">point_defect_diffusion calculation style</a></li>
<li class="toctree-l2"><a class="reference internal" href="notebook/point_defect_static.html">point_defect_static calculation style</a></li>
<li class="toctree-l2"><a class="reference internal" href="notebook/relax_box.html">relax_box calculation style</a></li>
<li class="toctree-l2"><a class="reference internal" href="notebook/relax_dynamic.html">relax_dynamic calculation style</a></li>
<li class="toctree-l2"><a class="reference internal" href="notebook/relax_static.html">relax_static calculation style</a></li>
<li class="toctree-l2"><a class="reference internal" href="notebook/stacking_fault_map_2D.html">stacking_fault_map_2D calculation style</a></li>
<li class="toctree-l2"><a class="reference internal" href="notebook/stacking_fault_static.html">stacking_fault_static calculation style</a></li>
<li class="toctree-l2"><a class="reference internal" href="notebook/surface_energy_static.html">surface_energy_static calculation style</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="record_styles.html">Record Styles</a><ul>
<li class="toctree-l2"><a class="reference internal" href="record/PotentialProperties/index.html">PotentialProperties</a></li>
<li class="toctree-l2"><a class="reference internal" href="record/calculation_E_vs_r_scan/index.html">calculation_E_vs_r_scan</a></li>
<li class="toctree-l2"><a class="reference internal" href="record/calculation_crystal_space_group/index.html">calculation_crystal_space_group</a></li>
<li class="toctree-l2"><a class="reference internal" href="record/calculation_diatom_scan/index.html">calculation_diatom_scan</a></li>
<li class="toctree-l2"><a class="reference internal" href="record/calculation_dislocation_SDVPN/index.html">calculation_dislocation_SDVPN</a></li>
<li class="toctree-l2"><a class="reference internal" href="record/calculation_dislocation_monopole/index.html">calculation_dislocation_monopole</a></li>
<li class="toctree-l2"><a class="reference internal" href="record/calculation_dislocation_periodic_array/index.html">calculation_dislocation_periodic_array</a></li>
<li class="toctree-l2"><a class="reference internal" href="record/calculation_elastic_constants_static/index.html">calculation_elastic_constants_static</a></li>
<li class="toctree-l2"><a class="reference internal" href="record/calculation_isolated_atom/index.html">calculation_isolated_atom</a></li>
<li class="toctree-l2"><a class="reference internal" href="record/calculation_relax_box/index.html">calculation_relax_box</a></li>
<li class="toctree-l2"><a class="reference internal" href="record/calculation_relax_dynamic/index.html">calculation_relax_dynamic</a></li>
<li class="toctree-l2"><a class="reference internal" href="record/calculation_relax_static/index.html">calculation_relax_static</a></li>
<li class="toctree-l2"><a class="reference internal" href="record/calculation_stacking_fault_map_2D/index.html">calculation_stacking_fault_map_2D</a></li>
<li class="toctree-l2"><a class="reference internal" href="record/calculation_stacking_fault_static/index.html">calculation_stacking_fault_static</a></li>
<li class="toctree-l2"><a class="reference internal" href="record/calculation_surface_energy_static/index.html">calculation_surface_energy_static</a></li>
<li class="toctree-l2"><a class="reference internal" href="record/crystal_prototype/index.html">crystal_prototype</a></li>
<li class="toctree-l2"><a class="reference internal" href="record/dislocation/index.html">dislocation</a></li>
<li class="toctree-l2"><a class="reference internal" href="record/free_surface/index.html">free_surface</a></li>
<li class="toctree-l2"><a class="reference internal" href="record/point_defect/index.html">point_defect</a></li>
<li class="toctree-l2"><a class="reference internal" href="record/potential_LAMMPS/index.html">potential_LAMMPS</a></li>
<li class="toctree-l2"><a class="reference internal" href="record/potential_openKIM_LAMMPS/index.html">potential_openKIM_LAMMPS</a></li>
<li class="toctree-l2"><a class="reference internal" href="record/potential_users_LAMMPS/index.html">potential_users_LAMMPS</a></li>
<li class="toctree-l2"><a class="reference internal" href="record/reference_crystal/index.html">reference_crystal</a></li>
<li class="toctree-l2"><a class="reference internal" href="record/relaxed_crystal/index.html">relaxed_crystal</a></li>
<li class="toctree-l2"><a class="reference internal" href="record/stacking_fault/index.html">stacking_fault</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="database_styles.html">Database Styles</a><ul>
<li class="toctree-l2"><a class="reference internal" href="database/cdcs/index.html">cdcs</a></li>
<li class="toctree-l2"><a class="reference internal" href="database/json/index.html">json</a></li>
<li class="toctree-l2"><a class="reference internal" href="database/local/index.html">local</a></li>
<li class="toctree-l2"><a class="reference internal" href="database/mdcs/index.html">mdcs</a></li>
<li class="toctree-l2"><a class="reference internal" href="database/mongo/index.html">mongo</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div class="section" id="code-documentation">
<h2>Code Documentation<a class="headerlink" href="#code-documentation" title="Permalink to this headline">¶</a></h2>
<div class="toctree-wrapper compound">
<ul>
<li class="toctree-l1"><a class="reference internal" href="iprPy/index.html">iprPy package</a><ul>
<li class="toctree-l2"><a class="reference internal" href="iprPy/index.html#subpackages">Subpackages</a><ul>
<li class="toctree-l3"><a class="reference internal" href="iprPy/calculation.html">iprPy.calculation package</a></li>
<li class="toctree-l3"><a class="reference internal" href="iprPy/database.html">iprPy.database package</a></li>
<li class="toctree-l3"><a class="reference internal" href="iprPy/input.html">iprPy.input package</a></li>
<li class="toctree-l3"><a class="reference internal" href="iprPy/record.html">iprPy.record package</a></li>
<li class="toctree-l3"><a class="reference internal" href="iprPy/tools.html">iprPy.tools package</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="iprPy/index.html#module-iprPy">Module contents</a></li>
</ul>
</li>
</ul>
</div>
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<div class="section" id="indices-and-tables">
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